data_UPR
# 
_chem_comp.id                                    UPR 
_chem_comp.name                                  "2'-DEOXYURIDINE-5'-ALPHA,BETA-AMINOPHOSPHORANE-TRIPHOSPHATE" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C9 H18 N3 O14 P3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2003-12-26 
_chem_comp.pdbx_modified_date                    2018-09-25 
_chem_comp.pdbx_ambiguous_flag                   N 
_chem_comp.pdbx_release_status                   OBS 
_chem_comp.pdbx_replaced_by                      ? 
_chem_comp.pdbx_replaces                         ? 
_chem_comp.formula_weight                        485.172 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     UPR 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        Corina 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        ? 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
# 
loop_
_chem_comp_atom.comp_id 
_chem_comp_atom.atom_id 
_chem_comp_atom.alt_atom_id 
_chem_comp_atom.type_symbol 
_chem_comp_atom.charge 
_chem_comp_atom.pdbx_align 
_chem_comp_atom.pdbx_aromatic_flag 
_chem_comp_atom.pdbx_leaving_atom_flag 
_chem_comp_atom.pdbx_stereo_config 
_chem_comp_atom.model_Cartn_x 
_chem_comp_atom.model_Cartn_y 
_chem_comp_atom.model_Cartn_z 
_chem_comp_atom.pdbx_model_Cartn_x_ideal 
_chem_comp_atom.pdbx_model_Cartn_y_ideal 
_chem_comp_atom.pdbx_model_Cartn_z_ideal 
_chem_comp_atom.pdbx_component_atom_id 
_chem_comp_atom.pdbx_component_comp_id 
_chem_comp_atom.pdbx_ordinal 
UPR PA     PA     P 0 1 N N N -9.241  60.498 31.229 1.560  2.368  -0.390 PA     UPR 1  
UPR O1A    O1A    O 0 1 N N N -10.604 60.802 31.981 2.680  2.503  -1.688 O1A    UPR 2  
UPR O2A    O2A    O 0 1 N N N -8.333  61.640 30.616 2.120  2.406  1.236  O2A    UPR 3  
UPR O3A    O3A    O 0 1 N N N -8.426  60.756 32.926 1.379  4.078  -0.367 O3A    UPR 4  
UPR N3A    N3A    N 0 1 N N N -10.143 60.067 29.638 1.750  0.568  -0.413 N3A    UPR 5  
UPR PB     PB     P 0 1 N N N -11.790 59.995 29.494 3.340  0.126  -0.083 PB     UPR 6  
UPR O1B    O1B    O 0 1 N N N -12.533 61.168 30.135 4.233  0.676  -1.127 O1B    UPR 7  
UPR O2B    O2B    O 0 1 N N N -11.821 59.911 28.053 3.772  0.708  1.355  O2B    UPR 8  
UPR O3B    O3B    O 0 1 N N N -12.267 58.608 30.165 3.458  -1.480 -0.068 O3B    UPR 9  
UPR PG     PG     P 0 1 N N N -13.087 58.513 31.556 4.670  -2.510 0.179  PG     UPR 10 
UPR O2G    O2G    O 0 1 N N N -12.542 59.381 32.642 5.456  -2.074 1.355  O2G    UPR 11 
UPR O1G    O1G    O 0 1 N N N -14.537 58.926 31.351 4.077  -3.983 0.447  O1G    UPR 12 
UPR O3G    O3G    O 0 1 N N N -12.960 57.059 31.983 5.621  -2.543 -1.120 O3G    UPR 13 
UPR "C5'"  "C5'"  C 0 1 N N N -9.126  57.961 31.727 -0.947 2.252  0.447  "C5'"  UPR 14 
UPR "O5'"  "O5'"  O 0 1 N N N -8.510  59.070 31.114 -0.120 2.195  -0.717 "O5'"  UPR 15 
UPR "C4'"  "C4'"  C 0 1 N N R -7.994  57.059 32.099 -2.418 2.172  0.031  "C4'"  UPR 16 
UPR "O4'"  "O4'"  O 0 1 N N N -7.277  56.651 30.970 -2.717 0.878  -0.535 "O4'"  UPR 17 
UPR "C3'"  "C3'"  C 0 1 N N S -7.059  57.466 33.199 -3.341 2.246  1.273  "C3'"  UPR 18 
UPR "O3'"  "O3'"  O 0 1 N N N -7.506  57.332 34.544 -3.617 3.604  1.624  "O3'"  UPR 19 
UPR "C2'"  "C2'"  C 0 1 N N N -5.738  56.846 32.812 -4.621 1.535  0.770  "C2'"  UPR 20 
UPR "C1'"  "C1'"  C 0 1 N N R -5.906  56.414 31.349 -4.137 0.690  -0.425 "C1'"  UPR 21 
UPR N1     N1     N 0 1 N N N -5.016  57.284 30.627 -4.436 -0.725 -0.188 N1     UPR 22 
UPR C2     C2     C 0 1 N N N -3.790  56.836 30.193 -5.303 -1.367 -0.992 C2     UPR 23 
UPR O2     O2     O 0 1 N N N -3.497  55.620 30.319 -5.829 -0.765 -1.908 O2     UPR 24 
UPR N3     N3     N 0 1 N N N -2.981  57.680 29.557 -5.595 -2.666 -0.796 N3     UPR 25 
UPR C4     C4     C 0 1 N N N -3.255  58.984 29.403 -5.020 -3.348 0.215  C4     UPR 26 
UPR O4     O4     O 0 1 N N N -2.425  59.719 28.809 -5.284 -4.523 0.392  O4     UPR 27 
UPR C5     C5     C 0 1 N N N -4.446  59.454 29.856 -4.106 -2.684 1.068  C5     UPR 28 
UPR C6     C6     C 0 1 N N N -5.350  58.598 30.484 -3.826 -1.382 0.846  C6     UPR 29 
UPR H1A    H1A    H 0 1 N N N -11.109 60.001 32.058 2.271  2.472  -2.565 H1A    UPR 30 
UPR H2A    H2A    H 0 1 N N N -7.566  61.252 30.211 1.855  1.639  1.762  H2A    UPR 31 
UPR H3A    H3A    H 0 1 N N N -7.487  60.637 32.848 1.918  4.540  -1.025 H3A    UPR 32 
UPR H2     H2     H 0 1 N N N -9.842  60.743 28.965 1.111  0.129  0.232  H2     UPR 33 
UPR H2B    H2B    H 0 1 N N N -12.325 60.636 27.704 3.229  0.388  2.088  H2B    UPR 34 
UPR H1G    H1G    H 0 1 N N N -14.755 59.629 31.952 4.753  -4.656 0.604  H1G    UPR 35 
UPR H3G    H3G    H 0 1 N N N -12.563 57.015 32.845 5.171  -2.820 -1.930 H3G    UPR 36 
UPR "H5'1" "H5'1" H 0 0 N N N -9.685  58.273 32.622 -0.710 1.416  1.104  "H5'1" UPR 37 
UPR "H5'2" "H5'2" H 0 0 N N N -9.808  57.459 31.025 -0.769 3.190  0.973  "H5'2" UPR 38 
UPR "H4'"  "H4'"  H 0 1 N N N -8.483  56.150 32.479 -2.659 2.965  -0.677 "H4'"  UPR 39 
UPR H1     H1     H 0 1 N N N -6.910  58.545 33.049 -2.904 1.710  2.116  H1     UPR 40 
UPR "H3'"  "H3'"  H 0 1 N N N -6.822  57.623 35.136 -4.191 3.702  2.396  "H3'"  UPR 41 
UPR "H2'1" "H2'1" H 0 0 N N N -4.925  57.581 32.906 -5.033 0.894  1.549  "H2'1" UPR 42 
UPR "H2'2" "H2'2" H 0 0 N N N -5.520  55.975 33.448 -5.361 2.266  0.445  "H2'2" UPR 43 
UPR "H1'"  "H1'"  H 0 1 N N N -5.628  55.356 31.229 -4.627 1.026  -1.339 "H1'"  UPR 44 
UPR HN3    HN3    H 0 1 N N N -2.128  57.325 29.175 -6.223 -3.114 -1.385 HN3    UPR 45 
UPR H5     H5     H 0 1 N N N -4.694  60.497 29.729 -3.635 -3.213 1.883  H5     UPR 46 
UPR H6     H6     H 0 1 N N N -6.296  58.969 30.850 -3.128 -0.860 1.484  H6     UPR 47 
# 
loop_
_chem_comp_bond.comp_id 
_chem_comp_bond.atom_id_1 
_chem_comp_bond.atom_id_2 
_chem_comp_bond.value_order 
_chem_comp_bond.pdbx_aromatic_flag 
_chem_comp_bond.pdbx_stereo_config 
_chem_comp_bond.pdbx_ordinal 
UPR PA    O1A    SING N N 1  
UPR PA    O2A    SING N N 2  
UPR PA    O3A    SING N N 3  
UPR PA    N3A    SING N N 4  
UPR PA    "O5'"  SING N N 5  
UPR O1A   H1A    SING N N 6  
UPR O2A   H2A    SING N N 7  
UPR O3A   H3A    SING N N 8  
UPR N3A   PB     SING N N 9  
UPR N3A   H2     SING N N 10 
UPR PB    O1B    DOUB N N 11 
UPR PB    O2B    SING N N 12 
UPR PB    O3B    SING N N 13 
UPR O2B   H2B    SING N N 14 
UPR O3B   PG     SING N N 15 
UPR PG    O2G    DOUB N N 16 
UPR PG    O1G    SING N N 17 
UPR PG    O3G    SING N N 18 
UPR O1G   H1G    SING N N 19 
UPR O3G   H3G    SING N N 20 
UPR "C5'" "O5'"  SING N N 21 
UPR "C5'" "C4'"  SING N N 22 
UPR "C5'" "H5'1" SING N N 23 
UPR "C5'" "H5'2" SING N N 24 
UPR "C4'" "O4'"  SING N N 25 
UPR "C4'" "C3'"  SING N N 26 
UPR "C4'" "H4'"  SING N N 27 
UPR "O4'" "C1'"  SING N N 28 
UPR "C3'" "O3'"  SING N N 29 
UPR "C3'" "C2'"  SING N N 30 
UPR "C3'" H1     SING N N 31 
UPR "O3'" "H3'"  SING N N 32 
UPR "C2'" "C1'"  SING N N 33 
UPR "C2'" "H2'1" SING N N 34 
UPR "C2'" "H2'2" SING N N 35 
UPR "C1'" N1     SING N N 36 
UPR "C1'" "H1'"  SING N N 37 
UPR N1    C2     SING N N 38 
UPR N1    C6     SING N N 39 
UPR C2    O2     DOUB N N 40 
UPR C2    N3     SING N N 41 
UPR N3    C4     SING N N 42 
UPR N3    HN3    SING N N 43 
UPR C4    O4     DOUB N N 44 
UPR C4    C5     SING N N 45 
UPR C5    C6     DOUB N N 46 
UPR C5    H5     SING N N 47 
UPR C6    H6     SING N N 48 
# 
loop_
_pdbx_chem_comp_descriptor.comp_id 
_pdbx_chem_comp_descriptor.type 
_pdbx_chem_comp_descriptor.program 
_pdbx_chem_comp_descriptor.program_version 
_pdbx_chem_comp_descriptor.descriptor 
UPR SMILES           ACDLabs              12.01 "P(O)(O)(O)(NP(=O)(O)OP(=O)(O)O)OCC1OC(CC1O)N2C(=O)NC(=O)C=C2"                                                                                                                                
UPR InChI            InChI                1.03  "InChI=1S/C9H18N3O14P3/c13-5-3-8(12-2-1-7(14)10-9(12)15)25-6(5)4-24-29(21,22,23)11-27(16,17)26-28(18,19)20/h1-2,5-6,8,13,21-23H,3-4H2,(H,10,14,15)(H2,11,16,17)(H2,18,19,20)/t5-,6+,8+/m0/s1" 
UPR InChIKey         InChI                1.03  VZYHSAMJZCSQOU-SHYZEUOFSA-N                                                                                                                                                                   
UPR SMILES_CANONICAL CACTVS               3.385 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)(O)N[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O"                                                                                                                
UPR SMILES           CACTVS               3.385 "O[CH]1C[CH](O[CH]1CO[P](O)(O)(O)N[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O"                                                                                                                     
UPR SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)COP(N[P@@](=O)(O)OP(=O)(O)O)(O)(O)O)O"                                                                                                                 
UPR SMILES           "OpenEye OEToolkits" 1.7.6 "C1C(C(OC1N2C=CC(=O)NC2=O)COP(NP(=O)(O)OP(=O)(O)O)(O)(O)O)O"                                                                                                                                  
# 
loop_
_pdbx_chem_comp_identifier.comp_id 
_pdbx_chem_comp_identifier.type 
_pdbx_chem_comp_identifier.program 
_pdbx_chem_comp_identifier.program_version 
_pdbx_chem_comp_identifier.identifier 
UPR "SYSTEMATIC NAME" ACDLabs              12.01 "2'-deoxy-5'-O-[(3R)-1,1,1,3-tetrahydroxy-3-oxo-3-(phosphonooxy)-1lambda~5~,3lambda~5~-diphosphazan-1-yl]uridine"                                           
UPR "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "N-[[(2R,3S,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-tris(oxidanyl)-$l^{5}-phosphanyl]-phosphonooxy-phosphonamidic acid" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
UPR "Create component"   2003-12-26 RCSB 
UPR "Modify descriptor"  2011-06-04 RCSB 
UPR "Obsolete component" 2018-09-25 RCSB 
# 
